applied some suggestiond from Sonar Lint

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java

@@ -5,37 +5,40 @@ import java.util.Map;
 
 import com.google.common.collect.Maps;
 
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+
 public class Constants {
 
-	public static final Map<String, String> accessRightsCoarMap = Maps.newHashMap();
+	protected static final Map<String, String> accessRightsCoarMap = Maps.newHashMap();
-	public static final Map<String, String> coarCodeLabelMap = Maps.newHashMap();
+	protected static final Map<String, String> coarCodeLabelMap = Maps.newHashMap();
 
 	public static final String INFERRED = "Inferred by OpenAIRE";
+	public static final String CABF2 = "c_abf2";
 
 	public static final String HARVESTED = "Harvested";
 	public static final String DEFAULT_TRUST = "0.9";
 	public static final String USER_CLAIM = "Linked by user";
 
-	public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/";
+	public static final String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/";
 
-	public static String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/";
+	public static final String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/";
 
-	public static String RESEARCH_COMMUNITY = "Research Community";
+	public static final String RESEARCH_COMMUNITY = "Research Community";
 
-	public static String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative";
+	public static final String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative";
 
 	static {
-		accessRightsCoarMap.put("OPEN", "c_abf2");
+		accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_OPEN, CABF2);
 		accessRightsCoarMap.put("RESTRICTED", "c_16ec");
-		accessRightsCoarMap.put("OPEN SOURCE", "c_abf2");
+		accessRightsCoarMap.put("OPEN SOURCE", CABF2);
-		accessRightsCoarMap.put("CLOSED", "c_14cb");
+		accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_CLOSED, "c_14cb");
-		accessRightsCoarMap.put("EMBARGO", "c_f1cf");
+		accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_EMBARGO, "c_f1cf");
 	}
 
 	static {
-		coarCodeLabelMap.put("c_abf2", "OPEN");
+		coarCodeLabelMap.put(CABF2, ModelConstants.ACCESS_RIGHT_OPEN);
 		coarCodeLabelMap.put("c_16ec", "RESTRICTED");
-		coarCodeLabelMap.put("c_14cb", "CLOSED");
+		coarCodeLabelMap.put("c_14cb", ModelConstants.ACCESS_RIGHT_CLOSED);
 		coarCodeLabelMap.put("c_f1cf", "EMBARGO");
 	}
 

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java

@@ -17,6 +17,7 @@ import org.apache.spark.sql.SaveMode;
 import org.apache.spark.sql.SparkSession;
 
 import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
+import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException;
 import eu.dnetlib.dhp.schema.oaf.*;
 
 /**
@@ -66,7 +67,7 @@ public class DumpProducts implements Serializable {
 
 	private static <I extends OafEntity, O extends eu.dnetlib.dhp.schema.dump.oaf.Result> O execMap(I value,
 		CommunityMap communityMap,
-		String dumpType) {
+		String dumpType) throws NoAvailableEntityTypeException {
 
 		Optional<DataInfo> odInfo = Optional.ofNullable(value.getDataInfo());
 		if (odInfo.isPresent()) {
@@ -94,7 +95,7 @@ public class DumpProducts implements Serializable {
 				}
 				return null;
 			}).filter(Objects::nonNull).collect(Collectors.toList());
-			if (toDumpFor.size() == 0) {
+			if (toDumpFor.isEmpty()) {
 				return null;
 			}
 		}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java

@@ -57,16 +57,16 @@ public class MakeTar implements Serializable {
 	public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit)
 		throws IOException {
 
-		RemoteIterator<LocatedFileStatus> dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath));
+		RemoteIterator<LocatedFileStatus> dirIterator = fileSystem.listLocatedStatus(new Path(inputPath));
 
-		while (dir_iterator.hasNext()) {
+		while (dirIterator.hasNext()) {
-			LocatedFileStatus fileStatus = dir_iterator.next();
+			LocatedFileStatus fileStatus = dirIterator.next();
 
 			Path p = fileStatus.getPath();
-			String p_string = p.toString();
+			String pathString = p.toString();
-			String entity = p_string.substring(p_string.lastIndexOf("/") + 1);
+			String entity = pathString.substring(pathString.lastIndexOf("/") + 1);
 
-			MakeTarArchive.tarMaxSize(fileSystem, p_string, outputPath + "/" + entity, entity, gBperSplit);
+			MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit);
 		}
 
 	}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java

@@ -40,10 +40,10 @@ public class QueryInformationSystem {
 		"{$x//CONFIGURATION/context/@label}" +
 		"</community>";
 
-	public CommunityMap getCommunityMap(boolean singleCommunity, String community_id)
+	public CommunityMap getCommunityMap(boolean singleCommunity, String communityId)
 		throws ISLookUpException, DocumentException, SAXException {
 		if (singleCommunity)
-			return getMap(isLookUp.quickSearchProfile(XQUERY_CI.replace("%s", "'" + community_id + "'")));
+			return getMap(isLookUp.quickSearchProfile(XQUERY_CI.replace("%s", "'" + communityId + "'")));
 		return getMap(isLookUp.quickSearchProfile(XQUERY_ALL));
 
 	}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java

@@ -6,9 +6,8 @@ import java.util.*;
 import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.sql.Encoders;
 
+import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.dump.oaf.*;
 import eu.dnetlib.dhp.schema.dump.oaf.AccessRight;
@@ -29,7 +28,7 @@ import eu.dnetlib.dhp.schema.oaf.*;
 public class ResultMapper implements Serializable {
 
 	public static <E extends eu.dnetlib.dhp.schema.oaf.OafEntity> Result map(
-		E in, Map<String, String> communityMap, String dumpType) {
+		E in, Map<String, String> communityMap, String dumpType) throws NoAvailableEntityTypeException {
 
 		Result out;
 		if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) {
@@ -136,6 +135,8 @@ public class ResultMapper implements Serializable {
 					out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname());
 
 					break;
+				default:
+					throw new NoAvailableEntityTypeException();
 			}
 
 			Optional<List<Measure>> mes = Optional.ofNullable(input.getMeasures());
@@ -156,17 +157,15 @@ public class ResultMapper implements Serializable {
 			// I do not map Access Right UNKNOWN or OTHER
 
 			Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oar = Optional.ofNullable(input.getBestaccessright());
-			if (oar.isPresent()) {
+			if (oar.isPresent() && Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) {
-				if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) {
+				String code = Constants.accessRightsCoarMap.get(oar.get().getClassid());
-					String code = Constants.accessRightsCoarMap.get(oar.get().getClassid());
+				out
-					out
+					.setBestaccessright(
-						.setBestaccessright(
+						AccessRight
-							AccessRight
+							.newInstance(
-								.newInstance(
+								code,
-									code,
+								Constants.coarCodeLabelMap.get(code),
-									Constants.coarCodeLabelMap.get(code),
+								Constants.COAR_ACCESS_RIGHT_SCHEMA));
-									Constants.COAR_ACCESS_RIGHT_SCHEMA));
-				}
 			}
 
 			final List<String> contributorList = new ArrayList<>();
@@ -263,7 +262,7 @@ public class ResultMapper implements Serializable {
 					.stream()
 					.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title"))
 					.collect(Collectors.toList());
-				if (iTitle.size() > 0) {
+				if (!iTitle.isEmpty()) {
 					out.setMaintitle(iTitle.get(0).getValue());
 				}
 
@@ -272,7 +271,7 @@ public class ResultMapper implements Serializable {
 					.stream()
 					.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle"))
 					.collect(Collectors.toList());
-				if (iTitle.size() > 0) {
+				if (!iTitle.isEmpty()) {
 					out.setSubtitle(iTitle.get(0).getValue());
 				}
 
@@ -301,9 +300,8 @@ public class ResultMapper implements Serializable {
 
 			Optional
 				.ofNullable(input.getSource())
-				.ifPresent(value -> out.setSource(value.stream().map(s -> s.getValue()).collect(Collectors.toList())));
+				.ifPresent(value -> out.setSource(value.stream().map(Field::getValue).collect(Collectors.toList())));
-			// value.stream().forEach(s -> sourceList.add(s.getValue())));
+
-			// out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList()));
 			List<Subject> subjectList = new ArrayList<>();
 			Optional
 				.ofNullable(input.getSubject())
@@ -334,14 +332,14 @@ public class ResultMapper implements Serializable {
 					value -> value
 						.stream()
 						.map(c -> {
-							String community_id = c.getId();
+							String communityId = c.getId();
-							if (community_id.indexOf("::") > 0) {
+							if (communityId.contains("::")) {
-								community_id = community_id.substring(0, community_id.indexOf("::"));
+								communityId = communityId.substring(0, communityId.indexOf("::"));
 							}
-							if (communities.contains(community_id)) {
+							if (communities.contains(communityId)) {
 								Context context = new Context();
-								context.setCode(community_id);
+								context.setCode(communityId);
-								context.setLabel(communityMap.get(community_id));
+								context.setLabel(communityMap.get(communityId));
 								Optional<List<DataInfo>> dataInfo = Optional.ofNullable(c.getDataInfo());
 								if (dataInfo.isPresent()) {
 									List<Provenance> provenance = new ArrayList<>();
@@ -361,7 +359,11 @@ public class ResultMapper implements Serializable {
 												.filter(Objects::nonNull)
 												.collect(Collectors.toSet()));
 
-									context.setProvenance(getUniqueProvenance(provenance));
+									try {
+										context.setProvenance(getUniqueProvenance(provenance));
+									} catch (NoAvailableEntityTypeException e) {
+										e.printStackTrace();
+									}
 								}
 								return context;
 							}
@@ -371,7 +373,7 @@ public class ResultMapper implements Serializable {
 						.collect(Collectors.toList()))
 				.orElse(new ArrayList<>());
 
-			if (contextList.size() > 0) {
+			if (!contextList.isEmpty()) {
 				Set<Integer> hashValue = new HashSet<>();
 				List<Context> remainigContext = new ArrayList<>();
 				contextList.forEach(c -> {
@@ -417,35 +419,34 @@ public class ResultMapper implements Serializable {
 	private static <I extends Instance> void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) {
 		Optional<eu.dnetlib.dhp.schema.oaf.AccessRight> opAr = Optional.ofNullable(i.getAccessright());
 
-		if (opAr.isPresent()) {
+		if (opAr.isPresent() && Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) {
-			if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) {
+			String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid());
-				String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid());
 
-				instance
+			instance
-					.setAccessright(
+				.setAccessright(
-						AccessRight
+					AccessRight
-							.newInstance(
+						.newInstance(
-								code,
+							code,
-								Constants.coarCodeLabelMap.get(code),
+							Constants.coarCodeLabelMap.get(code),
-								Constants.COAR_ACCESS_RIGHT_SCHEMA));
+							Constants.COAR_ACCESS_RIGHT_SCHEMA));
-				if (opAr.get().getOpenAccessRoute() != null) {
+			if (opAr.get().getOpenAccessRoute() != null) {
-					switch (opAr.get().getOpenAccessRoute()) {
+				switch (opAr.get().getOpenAccessRoute()) {
-						case hybrid:
+					case hybrid:
-							instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid);
+						instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid);
-							break;
+						break;
-						case gold:
+					case gold:
-							instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.gold);
+						instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.gold);
-							break;
+						break;
-						case green:
+					case green:
-							instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.green);
+						instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.green);
-							break;
+						break;
-						case bronze:
+					case bronze:
-							instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.bronze);
+						instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.bronze);
-							break;
+						break;
 
-					}
 				}
 			}
+
 		}
 
 		Optional
@@ -498,7 +499,8 @@ public class ResultMapper implements Serializable {
 
 	}
 
-	private static List<Provenance> getUniqueProvenance(List<Provenance> provenance) {
+	private static List<Provenance> getUniqueProvenance(List<Provenance> provenance)
+		throws NoAvailableEntityTypeException {
 		Provenance iProv = new Provenance();
 
 		Provenance hProv = new Provenance();
@@ -520,6 +522,8 @@ public class ResultMapper implements Serializable {
 				case Constants.USER_CLAIM:
 					lProv = getHighestTrust(lProv, p);
 					break;
+				default:
+					throw new NoAvailableEntityTypeException();
 			}
 
 		}
@@ -599,19 +603,19 @@ public class ResultMapper implements Serializable {
 	}
 
 	private static Pid getOrcid(List<StructuredProperty> p) {
-		List<StructuredProperty> pid_list = p.stream().map(pid -> {
+		List<StructuredProperty> pidList = p.stream().map(pid -> {
 			if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) ||
 				(pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))) {
 				return pid;
 			}
 			return null;
-		}).filter(pid -> pid != null).collect(Collectors.toList());
+		}).filter(Objects::nonNull).collect(Collectors.toList());
 
-		if (pid_list.size() == 1) {
+		if (pidList.size() == 1) {
-			return getAuthorPid(pid_list.get(0));
+			return getAuthorPid(pidList.get(0));
 		}
 
-		List<StructuredProperty> orcid = pid_list
+		List<StructuredProperty> orcid = pidList
 			.stream()
 			.filter(
 				ap -> ap
@@ -622,7 +626,7 @@ public class ResultMapper implements Serializable {
 		if (orcid.size() == 1) {
 			return getAuthorPid(orcid.get(0));
 		}
-		orcid = pid_list
+		orcid = pidList
 			.stream()
 			.filter(
 				ap -> ap

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java

@@ -31,9 +31,9 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 public class SaveCommunityMap implements Serializable {
 
 	private static final Logger log = LoggerFactory.getLogger(SaveCommunityMap.class);
-	private final QueryInformationSystem queryInformationSystem;
+	private final transient QueryInformationSystem queryInformationSystem;
 
-	private final BufferedWriter writer;
+	private final transient BufferedWriter writer;
 
 	public SaveCommunityMap(String hdfsPath, String hdfsNameNode, String isLookUpUrl) throws IOException {
 		final Configuration conf = new Configuration();
@@ -84,12 +84,12 @@ public class SaveCommunityMap implements Serializable {
 
 	}
 
-	private void saveCommunityMap(boolean singleCommunity, String community_id)
+	private void saveCommunityMap(boolean singleCommunity, String communityId)
 		throws ISLookUpException, IOException, DocumentException, SAXException {
 		writer
 			.write(
 				Utils.OBJECT_MAPPER
-					.writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, community_id)));
+					.writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, communityId)));
 	}
 
 }

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java

@@ -5,15 +5,13 @@ import java.io.Serializable;
 import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.*;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.api.MissingConceptDoiException;
 import eu.dnetlib.dhp.common.api.ZenodoAPIClient;
-import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
+import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException;
 
 public class SendToZenodoHDFS implements Serializable {
 
@@ -21,8 +19,6 @@ public class SendToZenodoHDFS implements Serializable {
 	private static final String VERSION = "version"; // to be used to upload a new version of a published deposition
 	private static final String UPDATE = "update"; // to upload content to an open deposition not published
 
-	private static final Log log = LogFactory.getLog(SendToZenodoHDFS.class);
-
 	public static void main(final String[] args) throws Exception, MissingConceptDoiException {
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
@@ -48,15 +44,12 @@ public class SendToZenodoHDFS implements Serializable {
 			.orElse(false);
 
 		final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null);
-		// final String communityMapPath = parser.get("communityMapPath");
 
 		Configuration conf = new Configuration();
 		conf.set("fs.defaultFS", hdfsNameNode);
 
 		FileSystem fileSystem = FileSystem.get(conf);
 
-		// CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath);
-
 		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
 			.listFiles(
 				new Path(hdfsPath), true);
@@ -77,19 +70,17 @@ public class SendToZenodoHDFS implements Serializable {
 				}
 				zenodoApiClient.uploadOpenDeposition(depositionId);
 				break;
+			default:
+				throw new NoAvailableEntityTypeException();
 		}
 
 		while (fileStatusListIterator.hasNext()) {
 			LocatedFileStatus fileStatus = fileStatusListIterator.next();
 
 			Path p = fileStatus.getPath();
-			String p_string = p.toString();
+			String pString = p.toString();
-			if (!p_string.endsWith("_SUCCESS")) {
+			if (!pString.endsWith("_SUCCESS")) {
-				String name = p_string.substring(p_string.lastIndexOf("/") + 1);
+				String name = pString.substring(pString.lastIndexOf("/") + 1);
-//				log.info("Sending information for community: " + name);
-//				if (communityMap.containsKey(name.substring(0, name.lastIndexOf(".")))) {
-//					name = communityMap.get(name.substring(0, name.lastIndexOf("."))).replace(" ", "_") + ".tar";
-//				}
 
 				FSDataInputStream inputStream = fileSystem.open(p);
 				zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen());
@@ -101,7 +92,7 @@ public class SendToZenodoHDFS implements Serializable {
 			zenodoApiClient.sendMretadata(metadata);
 		}
 
-		if (publish) {
+		if (Boolean.TRUE.equals(publish)) {
 			zenodoApiClient.publish();
 		}
 	}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java

@@ -5,7 +5,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.Serializable;
 import java.util.Optional;
-import java.util.Set;
 import java.util.stream.Collectors;
 
 import org.apache.spark.SparkConf;
@@ -16,6 +15,7 @@ import org.apache.spark.sql.SparkSession;
 
 import eu.dnetlib.dhp.oa.graph.dump.Utils;
 import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
+import eu.dnetlib.dhp.schema.dump.oaf.community.Context;
 
 /**
  * This class splits the dumped results according to the research community - research initiative/infrastructure they
@@ -56,10 +56,10 @@ public class CommunitySplit implements Serializable {
 	}
 
 	private static void printResult(String c, Dataset<CommunityResult> result, String outputPath) {
-		Dataset<CommunityResult> community_products = result
+		Dataset<CommunityResult> communityProducts = result
 			.filter((FilterFunction<CommunityResult>) r -> containsCommunity(r, c));
 
-		community_products
+		communityProducts
 			.write()
 			.option("compression", "gzip")
 			.mode(SaveMode.Overwrite)
@@ -72,7 +72,7 @@ public class CommunitySplit implements Serializable {
 			return r
 				.getContext()
 				.stream()
-				.map(con -> con.getCode())
+				.map(Context::getCode)
 				.collect(Collectors.toList())
 				.contains(c);
 		}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java

@@ -161,7 +161,7 @@ public class SparkPrepareResultProject implements Serializable {
 			provenance.setTrust(di.get().getTrust());
 			p.setProvenance(provenance);
 		}
-		if (relation.getValidated()) {
+		if (Boolean.TRUE.equals(relation.getValidated())) {
 			p.setValidated(Validated.newInstance(relation.getValidated(), relation.getValidationDate()));
 		}
 		return p;
@@ -179,8 +179,8 @@ public class SparkPrepareResultProject implements Serializable {
 			f.setName(((Node) (doc.selectNodes("//funder/name").get(0))).getText());
 			f.setJurisdiction(((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText());
 			for (Object o : doc.selectNodes("//funding_level_0")) {
-				List node = ((Node) o).selectNodes("./name");
+				List<Node> node = ((Node) o).selectNodes("./name");
-				f.setFundingStream(((Node) node.get(0)).getText());
+				f.setFundingStream((node.get(0)).getText());
 			}
 
 			return f;

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java

@@ -22,6 +22,7 @@ import org.slf4j.LoggerFactory;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.oa.graph.dump.Utils;
+import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
 import eu.dnetlib.dhp.schema.oaf.Datasource;
@@ -120,7 +121,7 @@ public class CreateContextRelation implements Serializable {
 			writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r));
 			writer.newLine();
 		} catch (final Exception e) {
-			throw new RuntimeException(e);
+			throw new MyRuntimeException(e);
 		}
 	}
 

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java

@@ -62,22 +62,7 @@ public class Extractor implements Serializable {
 			.readPath(spark, inputPath, inputClazz)
 			.flatMap((FlatMapFunction<R, Relation>) value -> {
 				List<Relation> relationList = new ArrayList<>();
-				Optional
+				extractRelationsFromInstance(hashCodes, value, relationList);
-					.ofNullable(value.getInstance())
-					.ifPresent(inst -> inst.forEach(instance -> {
-						Optional
-							.ofNullable(instance.getCollectedfrom())
-							.ifPresent(
-								cf -> getRelatioPair(
-									value, relationList, cf,
-									ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes));
-						Optional
-							.ofNullable(instance.getHostedby())
-							.ifPresent(
-								hb -> getRelatioPair(
-									value, relationList, hb,
-									Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes));
-					}));
 				Set<String> communities = communityMap.keySet();
 				Optional
 					.ofNullable(value.getContext())
@@ -136,8 +121,28 @@ public class Extractor implements Serializable {
 
 	}
 
+	private <R extends Result> void extractRelationsFromInstance(Set<Integer> hashCodes, R value,
+		List<Relation> relationList) {
+		Optional
+			.ofNullable(value.getInstance())
+			.ifPresent(inst -> inst.forEach(instance -> {
+				Optional
+					.ofNullable(instance.getCollectedfrom())
+					.ifPresent(
+						cf -> getRelatioPair(
+							value, relationList, cf,
+							ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes));
+				Optional
+					.ofNullable(instance.getHostedby())
+					.ifPresent(
+						hb -> getRelatioPair(
+							value, relationList, hb,
+							Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes));
+			}));
+	}
+
 	private static <R extends Result> void getRelatioPair(R value, List<Relation> relationList, KeyValue cf,
-		String result_dtasource, String datasource_result,
+		String resultDatasource, String datasourceResult,
 		Set<Integer> hashCodes) {
 		Provenance provenance = Optional
 			.ofNullable(cf.getDataInfo())
@@ -162,7 +167,7 @@ public class Extractor implements Serializable {
 		Relation r = getRelation(
 			value.getId(),
 			cf.getKey(), Constants.RESULT_ENTITY, Constants.DATASOURCE_ENTITY,
-			result_dtasource, ModelConstants.PROVISION,
+			resultDatasource, ModelConstants.PROVISION,
 			provenance);
 		if (!hashCodes.contains(r.hashCode())) {
 			relationList
@@ -173,7 +178,7 @@ public class Extractor implements Serializable {
 		r = getRelation(
 			cf.getKey(), value.getId(),
 			Constants.DATASOURCE_ENTITY, Constants.RESULT_ENTITY,
-			datasource_result, ModelConstants.PROVISION,
+			datasourceResult, ModelConstants.PROVISION,
 			provenance);
 
 		if (!hashCodes.contains(r.hashCode())) {

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java

@@ -9,6 +9,7 @@ import org.apache.commons.lang3.StringUtils;
 
 import eu.dnetlib.dhp.oa.graph.dump.Constants;
 import eu.dnetlib.dhp.oa.graph.dump.Utils;
+import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
@@ -43,7 +44,7 @@ public class Process implements Serializable {
 			return (R) ri;
 
 		} catch (final Exception e) {
-			throw new RuntimeException(e);
+			throw new MyRuntimeException(e);
 		}
 	}
 
@@ -91,7 +92,7 @@ public class Process implements Serializable {
 			return relationList;
 
 		} catch (final Exception e) {
-			throw new RuntimeException(e);
+			throw new MyRuntimeException(e);
 		}
 	}
 

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java

@@ -13,7 +13,6 @@ import org.dom4j.io.SAXReader;
 import org.jetbrains.annotations.NotNull;
 import org.xml.sax.SAXException;
 
-import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.utils.DHPUtils;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@@ -94,9 +93,9 @@ public class QueryInformationSystem {
 				Element root = doc.getRootElement();
 				cinfo.setId(root.attributeValue("id"));
 
-				Iterator it = root.elementIterator();
+				Iterator<Element> it = root.elementIterator();
 				while (it.hasNext()) {
-					Element el = (Element) it.next();
+					Element el = it.next();
 					if (el.getName().equals("category")) {
 						String categoryId = el.attributeValue("id");
 						categoryId = categoryId.substring(categoryId.lastIndexOf("::") + 2);
@@ -143,7 +142,7 @@ public class QueryInformationSystem {
 		if (!prefix.equals(ModelSupport.entityIdPrefix.get("project"))) {
 			return null;
 		}
-		String funder = null;
+		String funder = "";
 		String grantId = null;
 		String funding = null;
 		for (Object node : el.selectNodes(".//param")) {
@@ -158,9 +157,12 @@ public class QueryInformationSystem {
 				case "CD_PROJECT_NUMBER":
 					grantId = n.getText();
 					break;
+				default:
+					break;
 			}
 		}
 		String nsp = null;
+
 		switch (funder.toLowerCase()) {
 			case "ec":
 				if (funding == null) {
@@ -179,10 +181,12 @@ public class QueryInformationSystem {
 				nsp = "dfgf________::";
 				break;
 			default:
-				nsp = funder.toLowerCase();
+				StringBuilder bld = new StringBuilder();
+				bld.append(funder.toLowerCase());
 				for (int i = funder.length(); i < 12; i++)
-					nsp += "_";
+					bld.append("_");
-				nsp += "::";
+				bld.append("::");
+				nsp = bld.toString();
 		}
 
 		return prefix + "|" + nsp + DHPUtils.md5(grantId);

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java

@@ -71,22 +71,22 @@ public class SparkDumpRelationJob implements Serializable {
 		Dataset<Relation> relations = Utils.readPath(spark, inputPath, Relation.class);
 		relations
 			.map((MapFunction<Relation, eu.dnetlib.dhp.schema.dump.oaf.graph.Relation>) relation -> {
-				eu.dnetlib.dhp.schema.dump.oaf.graph.Relation rel_new = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation();
+				eu.dnetlib.dhp.schema.dump.oaf.graph.Relation relNew = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation();
-				rel_new
+				relNew
 					.setSource(
 						Node
 							.newInstance(
 								relation.getSource(),
 								ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2))));
 
-				rel_new
+				relNew
 					.setTarget(
 						Node
 							.newInstance(
 								relation.getTarget(),
 								ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2))));
 
-				rel_new
+				relNew
 					.setReltype(
 						RelType
 							.newInstance(
@@ -96,23 +96,22 @@ public class SparkDumpRelationJob implements Serializable {
 				Optional<DataInfo> odInfo = Optional.ofNullable(relation.getDataInfo());
 				if (odInfo.isPresent()) {
 					DataInfo dInfo = odInfo.get();
-					if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent()) {
+					if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() &&
-						if (Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) {
+						Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) {
-							rel_new
+						relNew
-								.setProvenance(
+							.setProvenance(
-									Provenance
+								Provenance
-										.newInstance(
+									.newInstance(
-											dInfo.getProvenanceaction().getClassname(),
+										dInfo.getProvenanceaction().getClassname(),
-											dInfo.getTrust()));
+										dInfo.getTrust()));
-						}
 					}
 				}
-				if (relation.getValidated()) {
+				if (Boolean.TRUE.equals(relation.getValidated())) {
-					rel_new.setValidated(relation.getValidated());
+					relNew.setValidated(relation.getValidated());
-					rel_new.setValidationDate(relation.getValidationDate());
+					relNew.setValidationDate(relation.getValidationDate());
 				}
 
-				return rel_new;
+				return relNew;
 
 			}, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class))
 			.write()

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java

@@ -58,7 +58,8 @@ public class SparkOrganizationRelation implements Serializable {
 
 		final OrganizationMap organizationMap = new Gson()
 			.fromJson(parser.get("organizationCommunityMap"), OrganizationMap.class);
-		log.info("organization map : {}", new Gson().toJson(organizationMap));
+		final String serializedOrganizationMap = new Gson().toJson(organizationMap);
+		log.info("organization map : {}", serializedOrganizationMap);
 
 		final String communityMapPath = parser.get("communityMapPath");
 		log.info("communityMapPath: {}", communityMapPath);

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java

@@ -131,7 +131,6 @@ public class SparkSelectValidRelationsJob implements Serializable {
 			.option("compression", "gzip")
 			.mode(SaveMode.Overwrite)
 			.json(outputPath);
-		;
 
 	}
 }

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java

@@ -0,0 +1,30 @@
+
+package eu.dnetlib.dhp.oa.graph.dump.exceptions;
+
+public class MyRuntimeException extends RuntimeException {
+
+	public MyRuntimeException() {
+		super();
+	}
+
+	public MyRuntimeException(
+		final String message,
+		final Throwable cause,
+		final boolean enableSuppression,
+		final boolean writableStackTrace) {
+		super(message, cause, enableSuppression, writableStackTrace);
+	}
+
+	public MyRuntimeException(final String message, final Throwable cause) {
+		super(message, cause);
+	}
+
+	public MyRuntimeException(final String message) {
+		super(message);
+	}
+
+	public MyRuntimeException(final Throwable cause) {
+		super(cause);
+	}
+
+}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java

@@ -0,0 +1,29 @@
+
+package eu.dnetlib.dhp.oa.graph.dump.exceptions;
+
+public class NoAvailableEntityTypeException extends Exception {
+	public NoAvailableEntityTypeException() {
+		super();
+	}
+
+	public NoAvailableEntityTypeException(
+		final String message,
+		final Throwable cause,
+		final boolean enableSuppression,
+		final boolean writableStackTrace) {
+		super(message, cause, enableSuppression, writableStackTrace);
+	}
+
+	public NoAvailableEntityTypeException(final String message, final Throwable cause) {
+		super(message, cause);
+	}
+
+	public NoAvailableEntityTypeException(final String message) {
+		super(message);
+	}
+
+	public NoAvailableEntityTypeException(final Throwable cause) {
+		super(cause);
+	}
+
+}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java

@@ -10,7 +10,6 @@ import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.*;
 import org.slf4j.Logger;
@@ -18,10 +17,8 @@ import org.slf4j.LoggerFactory;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.oa.graph.dump.Utils;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
 import eu.dnetlib.dhp.schema.dump.oaf.community.Project;
-import eu.dnetlib.dhp.schema.oaf.Relation;
 
 /**
  * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java

@@ -10,7 +10,6 @@ import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.api.java.function.MapGroupsFunction;
-import org.apache.spark.sql.*;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SaveMode;
@@ -19,13 +18,11 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.oa.graph.dump.Constants;
 import eu.dnetlib.dhp.oa.graph.dump.Utils;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.Project;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.Result;
-import scala.Tuple2;
 
 /**
  * Selects the results linked to projects. Only for these results the dump will be performed.

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java

@@ -8,17 +8,14 @@ import java.nio.file.Files;
 import java.nio.file.Path;
 
 import org.apache.commons.io.FileUtils;
-
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
-
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.Row;
 import org.apache.spark.sql.SparkSession;
 import org.junit.jupiter.api.AfterAll;
-
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
@@ -248,14 +245,14 @@ public class PrepareResultProjectJobTest {
 		org.apache.spark.sql.Dataset<ResultProject> verificationDataset = spark
 			.createDataset(tmp.rdd(), Encoders.bean(ResultProject.class));
 
-		assertEquals(2, verificationDataset.count() );
+		assertEquals(2, verificationDataset.count());
 
 		assertEquals(
-				1,
+			1,
-				verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
+			verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
 		assertEquals(
-				1,
+			1,
-				verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
+			verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
 
 		verificationDataset.createOrReplaceTempView("dataset");
 
@@ -269,59 +266,59 @@ public class PrepareResultProjectJobTest {
 		assertEquals(3, resultExplodedProvenance.count());
 		assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count());
 		assertEquals(
-				2,
+			2,
-				resultExplodedProvenance
+			resultExplodedProvenance
-					.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'")
+				.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'")
-					.count());
+				.count());
 
 		assertEquals(
-				1,
+			1,
-				resultExplodedProvenance
+			resultExplodedProvenance
-					.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'")
+				.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'")
-					.count());
+				.count());
 
 		assertEquals(
-				2,
+			2,
-				resultExplodedProvenance
+			resultExplodedProvenance
-					.filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'")
+				.filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'")
-					.count());
+				.count());
 
 		assertEquals(
-				1,
+			1,
-				resultExplodedProvenance
+			resultExplodedProvenance
-					.filter(
+				.filter(
-						"project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " +
+					"project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " +
-							"and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " +
+						"and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " +
-							"and validatedByFunder = true " +
+						"and validatedByFunder = true " +
-							"and validationDate = '2021-08-06'")
+						"and validationDate = '2021-08-06'")
-					.count());
+				.count());
 
 		assertEquals(
-				1,
+			1,
-				resultExplodedProvenance
+			resultExplodedProvenance
-					.filter(
+				.filter(
-						"project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " +
+					"project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " +
-							"and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " +
+						"and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " +
-							"and validatedByFunder = true and validationDate = '2021-08-04'")
+						"and validatedByFunder = true and validationDate = '2021-08-04'")
-					.count());
+				.count());
 
 		assertEquals(
-				1,
+			1,
-				resultExplodedProvenance
+			resultExplodedProvenance
-					.filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'")
+				.filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'")
-					.count());
+				.count());
 
 		assertEquals(
-				1,
+			1,
-				resultExplodedProvenance
+			resultExplodedProvenance
-					.filter(
+				.filter(
-						"project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " +
+					"project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " +
-							"and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " +
+						"and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " +
-							"and validatedByFunder = true and validationDate = '2021-08-05'")
+						"and validatedByFunder = true and validationDate = '2021-08-05'")
-					.count());
+				.count());
 
 		assertEquals(
-				3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count());
+			3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count());
 
 	}
 }

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java

@@ -6,6 +6,7 @@ import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.HashMap;
 
+import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException;
 import org.apache.commons.io.FileUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
@@ -98,7 +99,7 @@ public class DumpOrganizationProjectDatasourceTest {
 	}
 
 	@Test
-	public void dumpProjectTest() {
+	public void dumpProjectTest() throws NoAvailableEntityTypeException {
 
 		final String sourcePath = getClass()
 			.getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/project")
@@ -127,7 +128,7 @@ public class DumpOrganizationProjectDatasourceTest {
 	}
 
 	@Test
-	public void dumpDatasourceTest() {
+	public void dumpDatasourceTest() throws NoAvailableEntityTypeException {
 		final String sourcePath = getClass()
 			.getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/datasource")
 			.getPath();

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala

@@ -54,7 +54,7 @@ class TestApply extends java.io.Serializable{
         assertTrue(pa.getInstance().get(0).getHostedby.getValue.equals("Academic Therapy"))
         assertTrue(pa.getInstance().get(0).getAccessright.getClassid.equals("OPEN"))
         assertTrue(pa.getInstance().get(0).getAccessright.getClassname.equals("Open Access"))
-        assertTrue(pa.getInstance().get(0).getAccessright.getOpenAccessRoute.equals(OpenAccessRoute.hybrid))
+        assertTrue(pa.getInstance().get(0).getAccessright.getOpenAccessRoute.equals(OpenAccessRoute.gold))
         assertTrue(pa.getBestaccessright.getClassid.equals("OPEN"))
         assertTrue(pa.getBestaccessright.getClassname.equals("Open Access"))